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Data from: A High-Quality Genome Assembly from a Single, Field-collected Spotted Lanternfly (Lycorma delicatula) using the PacBio Sequel II System
OwnerUnited States Department of Agriculture - view all
Update frequencyunknown
Last updated10 months ago
Overview

A high-quality reference genome is an essential tool for applied and basic research on arthropods. Long-read sequencing technologies may be used to generate more complete and contiguous genome assemblies than alternate technologies, however, long-read methods have historically had greater input DNA requirements and higher costs than next generation sequencing, which are barriers to their use on many samples. Here, we present a 2.3 Gb de novo genome assembly of a field-collected adult female Spotted Lanternfly (Lycorma delicatula) using a single PacBio SMRT Cell. The Spotted Lanternfly is an invasive species recently discovered in the northeastern United States, threatening to damage economically important crop plants in the region. The DNA from one individual female specimen collected in Reading, Berks County, Pennsylvania was used to make one standard, size-selected library with an average DNA fragment size of ~20 kb. The library was run on one Sequel II SMRT Cell 8M, generating a total of 132 Gb of long-read sequences, of which 82 Gb were from unique library molecules, representing approximately 38x coverage of the genome. The assembly had high contiguity (contig N50 length = 1.5 Mb), completeness, and sequence level accuracy as estimated by conserved gene set analysis (96.8% of conserved genes both complete and without frame shift errors). Further, it was possible to segregate more than half of the diploid genome into the two separate haplotypes. The assembly also recovered two microbial symbiont genomes known to be associated with L. delicatula, each microbial genome being assembled into a single contig. We demonstrate that field-collected arthropods can be used for the rapid generation of high-quality genome assemblies, an attractive approach for projects on emerging invasive species, disease vectors, or conservation efforts of endangered species. Supporting files for the manuscript "A High-Quality Genome Assembly from a Single, Field-collected Spotted Lanternfly (Lycorma delicatula) using the PacBio Sequel II System", include several intermediate versions of the assembly (raw output from Falcon, raw output from Falcon unzip, etc.) as well as the final assembly primary contigs and haplotigs (for the regions of the genome that were phased).

NP304Spotted Lantern Flyag100pestgenomics
Additional Information
KeyValue
dcat_modified2023-06-23
dcat_publisher_nameAgricultural Research Service
guid9ff39222-988f-4e6c-9699-ea1e7f8c3f04
language
harvest_object_id39059b76-f4dd-4c62-af24-b475a574e053
harvest_source_id2c0b1e04-ba48-4488-9de5-0dab41f9913f
harvest_source_titleUSDA Open Data Catalog
Files
  • ZIP
    Final Assembly file
  • ZIP
    Falcon Raw assembly, polished with arrow
  • ZIP
    Fasta file of contig assemblies of the two symbiont genomes
  • PAF
    Haplotig placement file in PAF format
  • fasta
    Falcon Unzip assembly Polished with arrow
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